[ENH] Microscopy: Add IntendedFor metadata field to photo files

[mariehbourget]

closes #992

Dear BIDS community,

This PR address the issue in:

• Microscopy files of suffix _photo do not support a _run- entity. #992

... where there was no mechanism in microscopy to associated a photo of a sample to a specific run or modality (for example: a photo could be generated at each run). Our best option seems to be a JSON file associated to the photo with the IntendedFor metadata field, which I added in this PR.

Link to the rendered doc: https://bids-specification--1000.org.readthedocs.build/en/1000/04-modality-specific-files/10-microscopy.html#photos-of-the-samples-_photoextension

Please let me know your thoughts and suggestions, thank you!

Note: If we go with this, we will need to update the bids-validator with the addition of the JSON file for photo and its associated rules.

• validator: https://github.com/bids-standard/bids-validator/pull/1415
• examples: [ENH] Microscopy: Add photos and associated JSON files bids-examples#307

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.11%. Comparing base (4e9a872) to head (a402787).
Report is 1250 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1000      +/-   ##
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+ Coverage   70.16%   71.11%   +0.94%     
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  Files           9        9              
  Lines         952      952              
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+ Hits          668      677       +9     
+ Misses        284      275       -9     

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[satra]

while we are making changes to the json document, would there be some benefit to add the possibility of some field that describes details of acquisition.

examples:

• one can take a photo before and after clearing
• block-face image and then slice laid out image

at the simplest level an optional description field can be added.

cc: @LeeKamentsky @gmazzamuto

[LeeKamentsky]

This is kind of long-range, but it might be nice to place the photo in time with relation to the tissue protocol - somehow linking it to between two stages or after a stage. @satra is right about taking the photo before or after clearing - a huge difference in appearance and the intention of the photographer in picking the timing of the photo. I can imagine taking a picture of one of our slabs on the microscope stage would help us understand the orientation of the resulting image and other aspects.

[mariehbourget]

Great idea, thanks! I added a "PhotoDescription" field with example.

[mariehbourget]

I opened WIP PR for bids-examples (bids-standard/bids-examples#307) and bids-validator (https://github.com/bids-standard/bids-validator/pull/1415) associated with the changes.

[gmazzamuto]

That's seems a good idea! indeed we usually take photos of the samples before and after clearing. These were also uploaded to DANDI

[mariehbourget]

Hi everyone, it's been a while!
We are currently finalizing the validator PR https://github.com/bids-standard/bids-validator/pull/1415 associated with these changes.

So this PR is ready for review again.
As discussed, it adds:

• A JSON sidecar file to _photo files.
• 2 fields in this JSON: PhotoDescription and IntendedFor.

[sappelhoff]

the other modalities where "_photo" is used as a suffix file apparently don't (yet?) allow .json sidecars, but I see no reason why it shouldn't be the case.

LGTM

[sappelhoff]

@TheChymera I wanted to request you as a reviewer and then noticed that you are not yet part of the org, so I've sent you some invitations for that. Please check your inbox :-)

[Remi-Gau]

LGTM